Related papers: Cartesian Tree Subsequence Matching
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
Thin spanning trees lie at the intersection of graph theory, approximation algorithms, and combinatorial optimization. They are central to the long-standing \emph{thin tree conjecture}, which asks whether every $k$-edge-connected graph…
Min-Cut queries are fundamental: Preprocess an undirected edge-weighted graph, to quickly report a minimum-weight cut that separates a query pair of nodes $s,t$. The best data structure known for this problem simply builds a cut-equivalent…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
In the Minimum Consistent Subset (MCS) problem, we are presented with a connected simple undirected graph $G=(V,E)$, consisting of a vertex set $V$ of size $n$ and an edge set $E$. Each vertex in $V$ is assigned a color from the set…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
The Minimum Consistent Subset (MCS) problem arises naturally in the context of supervised clustering and instance selection. In supervised clustering, one aims to infer a meaningful partitioning of data using a small labeled subset.…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
This paper studies the performances of BERT combined with tree structure in short sentence ranking task. In retrieval-based question answering system, we retrieve the most similar question of the query question by ranking all the questions…
The palindromic tree (a.k.a. eertree) for a string $S$ of length $n$ is a tree-like data structure that represents the set of all distinct palindromic substrings of $S$, using $O(n)$ space [Rubinchik and Shur, 2018]. It is known that, when…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
The kTree problem is a special case of Subgraph Isomorphism where the pattern graph is a tree, that is, the input is an $n$-node graph $G$ and a $k$-node tree $T$, and the goal is to determine whether $G$ has a subgraph isomorphic to $T$.…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…